Genomic studies of low-biomass environments is often limited by the amount of DNA available, and one solution has been to use a whole genome amplification technique that uses phi29 DNA polymerase known as multiple displacement amplification (MDA). When used in single cell genomic studies, one noted drawback of the procedure has been amplification bias that…
100 Rhizobium Genomes Project on INRA’s MyCorWeb page
A joint venture has been established between the Centre for Rhizobium Studies (CRS) led by Dr Wayne Reeve at Murdoch University (Australia) and the Joint Genome Institute (JGI, USA) led by the Head of the Microbial Program Dr Nikos Kyrpides to completely decipher the genetic code for 100 geographically distinct root nodule rhizobial strains.’ Read more on the…
DOE’s Magellan cloud project on ESnet
We were glad to see DOE’s Magellan project getting some well-deserved recognition by the HPCwire Readers’ and Editors’ Choice Award at SC10 in New Orleans. Magellan investigates how cloud computing can help DOE researchers to manage the massive (and increasing) amount of data they generate in scientific collaborations. Magellan is a joint research project at…
Iowa colleges team with DOE JGI to Interpret-A-Genome
Augustana and two other Quad-City higher education institutions—Eastern Iowa Community College District and Black Hawk Community College—have partnered together to adopt the microbe Meiothermus ruber and join the Interpret a Genome project through the U.S. Department of Energy-Joint Genome Institute (DOE-JGI). Read more at the Aledo Times Record.
Award for DOE’s Magellan Cloud Computing Project
One of the first key users of NERSC’s Magellan cloud computing system was DOE’s Joint Genome Institute (JGI). In March, the facility had a sudden need for increased computing resources, and in less than three days, NERSC and JGI staff provisioned and configured hundreds of processor cores on the Magellan system to match the computing…
Making up the gut microbiome is a host-driven project
Baking sourdough bread requires a starter, and so do mammalian guts, which are first colonized by microbial communities from the mother and then acquire more microbes over time. These gut microbial communities are important for maintaining health and combating disease, and it’s why the Human Microbiome Project launched by the National Institutes of Health in…
DNA Sequencing at the JGI on PhysicsToday blog
According to the Department of Energy, 200 million base pairs were sequenced for all genome projects in the whole of 1998. By 2003 one large project alone, the DOE’s Joint Genome Institute (JGI), sequenced some 1.5 billion bases in a month. If the march of DNA sequencing had been increasing according to Moore’s law, then,…
JGI-Murdoch University rhizobial project
Rhizobia are soil bacteria that can form a symbiotic relationship with legumes such as common domesticated crops such as peas, beans or clovers. These symbiotic bacteria fix atmospheric nitrogen inside nodules formed on the legume roots contributing around 65% of the nitrogen currently used in agricultural production. A joint venture has been established between the…
Methanotroph Methylosinus trichosporium
Considered the second most important greenhouse gas, methane is 21 times more potent than carbon dioxide. Methane-oxidizing bacteria called methanotrophs help reduce levels of atmospheric methane. To better understand the bacteria involved in the global methane cycle, the DOE JGI sequenced, assembled and annotated the genome of Methylosinus trichosporium OB3b. The project was led by…
JGI sequencers on GenomeWeb
The US Department of Energy Joint Genome Institute now uses a collection of next-gen sequencers from a variety of firms, following the phasing out of its Sanger machines. Read more on GenomeWeb.